Adding examples for remove connections for 2 circuits (#1)

* adding examples for removing connection. one for sscx one for simple small circuit

* moved dev files, and updated structure of folder, removed some irrelevant files

* added README and had first successful conn_removal example under output/example_circuit_nodeA but the amount_pct is hard_coded in the code and structure is not clearly defined. TBF

* clean old files

* fixed config

* add readme, clean logs

* restructure remove conns

* update str comp for multipop

* remove extra notebook and clean the existing one

* add readme and move example circuit

* add readme and move example circuit 2

* update readme

* fixing conn_removal.py for edge case of connectome size smaller than nsplit and fixing examples

* fixing edge writer

* add copyright info

* fix notebook

* Stop tracking .txt log files in examples/ and update .gitignore and add readme under example circuits

* actually add readme under example circuits

* remove output/logs/ for examples

* Revert file to match upstream version

.gitignore

@@ -10,4 +10,16 @@ dist/
 build/
 connectome_manipulator.egg-info
 __pycache__
-examples/working_dir
+examples/working_dir
+
+# Ignore all .h5 files under examples
+examples/**/*.h5
+
+# Unignore specific folder (replace specific/folder with your folder path)
+!examples/circuits/**/*.h5
+
+# ignore dev files
+**/*.dev.*
+
+# ignore log files under examples
+examples/**/logs/*.txt

examples/README.md

@@ -3,7 +3,8 @@
 The following example notebooks demonstrate important use cases of the _Connectome-Manipulator_ framework:
 
 - <u>Example 1</u>: [Null manipulation](./null_manipulation/NullManipulationExample.ipynb)
+- <u>Example 2</u>: [Remove connections](./remove_connections/)
 
 - More to come...
 
-Copyright (c) 2024 Blue Brain Project/EPFL
+Copyright (c) 2024 Blue Brain Project/EPFL

examples/circuits/README.md

@@ -0,0 +1,8 @@
+## Example Circuits 
+
+This folder contains circuits that can be given to connectome manipulator as input. As a minimal use case, we added [a small SONATA circuit](./circuit_sonata_quick_scx_multi_circuit) from BlueCelluLab library:
+
+https://github.com/BlueBrain/BlueCelluLab/tree/main/examples/2-sonata-network
+
+
+The other examples can be accessed using the notebooks from each example.

examples/circuits/circuit_sonata_quick_scx_multi_circuit/.exception_node

@@ -0,0 +1 @@
+5

examples/circuits/circuit_sonata_quick_scx_multi_circuit/circuit_config.json

@@ -0,0 +1,63 @@
+{
+    "version": 2,
+    "node_sets_file": "./node_sets.json",
+    "networks": {
+        "nodes": [
+            {
+                "nodes_file": "nodes_A.h5",
+                "populations": {
+                    "NodeA": {
+                        "type": "biophysical",
+                        "morphologies_dir": "./components/CircuitA/morphologies/swc",
+                        "biophysical_neuron_models_dir": "./components/CircuitA/hoc",
+                        "alternate_morphologies": {
+                            "neurolucida-asc": "./components/CircuitA/morphologies/asc"
+                        }
+                    }
+                }
+            },
+            {
+                "nodes_file": "nodes_B.h5",
+                "populations": {
+                    "NodeB": {
+                        "type": "biophysical",
+                        "morphologies_dir": "./components/CircuitB/morphologies/swc",
+                        "biophysical_neuron_models_dir": "./components/CircuitB/hoc",
+                        "alternate_morphologies": {
+                            "neurolucida-asc": "./components/CircuitB/morphologies/asc"
+                        }
+                    }
+                }
+            }
+        ],
+        "edges": [
+            {
+                "edges_file": "local_edges_A.h5",
+                "populations": {
+                    "NodeA__NodeA__chemical": {
+                        "type": "chemical"
+                    }
+                }
+            },
+            {
+                "edges_file": "local_edges_B.h5",
+                "populations": {
+                    "NodeB__NodeB__chemical": {
+                        "type": "chemical"
+                    }
+                }
+            },
+            {
+                "edges_file": "edges_AB.h5",
+                "populations": {
+                    "NodeA__NodeB__chemical": {
+                        "type": "chemical"
+                    },
+                    "NodeB__NodeA__chemical": {
+                        "type": "chemical"
+                    }
+                }
+            }
+        ]
+    }
+}